def GetTransformationText_v1(callback, xmlPath):
htmlFilename = 'default-0.html'
pathParts = xmlPath.split('/')
rods_zone = pathParts[1]
transformationBasePath = '/' + rods_zone + '/yoda/transformations/default-1'
# Collect the transformation explanation text for the enduser.
data_size = getDataObjSize(callback, transformationBasePath, htmlFilename)
path = transformationBasePath + '/' + htmlFilename
# Open transformation information file.
ret_val = callback.msiDataObjOpen('objPath=' + path, 0)
fileHandle = ret_val['arguments'][1]
# Read data.
ret_val = callback.msiDataObjRead(fileHandle, data_size, irods_types.BytesBuf())
# Close transformation information file.
callback.msiDataObjClose(fileHandle, 0)
read_buf = ret_val['arguments'][2]
transformationText = ''.join(read_buf.buf)
return transformationText
def getJsonSchemaFromiRODSObject(path, callback):
"""
This rule gets a JSON schema stored as an iRODS object
:param path: Full path of the json file (/nlmumc/home/rods/weight.json)
:param callback:
:return: JSON formatted schema
"""
ret_val = callback.msiGetObjType(path, "")
type_file = ret_val['arguments'][1]
if type_file != '-d':
callback.msiExit("-1101000", "Only files in iRODS can be used for JSON storage")
return
# Open iRODS file
ret_val = callback.msiDataObjOpen("objPath=" + path, 0)
file_desc = ret_val['arguments'][1]
# Read iRODS file
ret_val = callback.msiDataObjRead(file_desc, 2 ** 31 - 1, irods_types.BytesBuf())
read_buf = ret_val['arguments'][2]
# Convert BytesBuffer to string
ret_val = callback.msiBytesBufToStr(read_buf, "")
output_json = ret_val['arguments'][1]
# Close iRODS file
callback.msiDataObjClose(file_desc, 0)
return output_json
def parseJson(callback, path):
# Retrieve JSON size.
coll_name, data_name = os.path.split(path)
data_size = getDataObjSize(callback, coll_name, data_name)
# Open JSON file.
ret_val = callback.msiDataObjOpen('objPath=' + path, 0)
fileHandle = ret_val['arguments'][1]
# Read JSON file.
ret_val = callback.msiDataObjRead(fileHandle, data_size, irods_types.BytesBuf())
# Close JSON file.
callback.msiDataObjClose(fileHandle, 0)
# Parse JSON.
read_buf = ret_val['arguments'][2]
jsonText = ''.join(read_buf.buf)
return json.loads(jsonText)
def parseMetadataXml(callback, path):
# Retrieve XML size.
coll_name, data_name = os.path.split(path)
data_size = getDataObjSize(callback, coll_name, data_name)
# Open metadata XML.
ret_val = callback.msiDataObjOpen('objPath=' + path, 0)
fileHandle = ret_val['arguments'][1]
# Read metadata XML.
ret_val = callback.msiDataObjRead(fileHandle, data_size, irods_types.BytesBuf())
# Close metadata XML.
callback.msiDataObjClose(fileHandle, 0)
# Parse XML.
read_buf = ret_val['arguments'][2]
xmlText = ''.join(read_buf.buf)
return ET.fromstring(xmlText)